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Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
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From: Pablo C. <pc...@cn...> - 2021-09-30 16:21:29
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Carlos, there is a chance that it may work if they haven't changed the "interface". For that, I think is better to move this discussion offline to avoid spamming others, and come back with a final solution. I'll write you a private email. On 30/9/21 15:52, Grigory Sharov wrote: > Hi, > > As I said earlier, the sphire plugin does not support cryolo 1.8, you > cannot install or/and use it inside Scipion. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I > removed it using pip uninstall cryolo) and put it to work inside > Scipion? > I tried to no use GPUs on cryolo picking, but I obtained the same > error. > Thanks again for the help. > Best regards, Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 3:26:53 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hi Carlos, > you are using NVIDIA GeForce RTX 3090 which is only supported by > cryolo 1.8. > > Have a look here: > https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 > <https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11> > > AFAIK, Scipion does not support this version yet. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks for all support. Cryolo training worked very well; > however, I'm facing some problems with cryolo picking. > I obtain this error: > /Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py > -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w > /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 > -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ > -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ > -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1/ > > When I execute in bash *conda activate cryolo-1.7.6 && which > cryolo_predict.py*, I obtain a normal response > //home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py/ > > I'm sorry, I thought that the problems were solved... > I attached the run.stderr and run.stdout files > Thanks again for the support. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 2:08:45 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Oh, that's great that it worked! > You are welcome! > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks so so much! > Cryolo is running now in Scipion. > Best regards, > Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 12:18:43 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Hi Carlos, > ok, can you run *pip uninstall cryolo* and then execute in > that order: > 1) *which cryolo_train.py * > 2)***conda activate**cryolo-1.7.6 && which cryolo_train.py* > > The first one should fail but the second one should show > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > When I run *conda activate* *cryolo-1.7.6 && which > cryolo_train.py* and *which cryolo_train.py *in bash I > receive as response: > //home/impmc/.local/bin/cryolo_train.py/ > > And when I go to this address, I can run all cryolo > python files normally. Best regards, Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 11:58:30 AM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Can you run *conda activate cryolo-1.7.6 && which > cryolo_train.py* ? > Can you also run *which cryolo_train.py *? (in case > you installed cryolo into conda base env) > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE > FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dears Grigory and Pablo, > > Sorry for the problems with conda; these things > are very recent to me; I'm still learning how to > deal with them. > And, thanks again for the messages and for the > support. > > About libcudnn.so.8; indeed there is no > libcudnn.so.8 installed in cryolo-1.7.6 > environment lib folder. There is only > libcudnn.so.7.1.2: > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 > It is possible to change to libcudnn.so.8 inside > these folders? > > About conda; Yes, cryolo 1.8 are using conda from > eman... I installed miniconda and anaconda3; > however when I type 'which conda', I have as only > response the conda from eman. > Best regards, > Carlos. > > ------------------------------------------------------------------------ > *From: *"Pablo Conesa" <pc...@cn... > <mailto:pc...@cn...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 10:29:11 AM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > I agree with Grigory, using eman2 conda is not a > good practice. > > Probably he did not decided that but Scipion > installer used the available one, and probably > that one was eman2 one. > > If you want to undo this you will need to install > miniconda, and have it available instead of eman2 one. > > "which conda" will tell you the available one. > > > On 29/9/21 18:54, Grigory Sharov wrote: > > Thanks! In run.stderr you can see the reason > it has failed: > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] > Could not load dynamic library > 'libcudnn.so.8'; dlerror: libcudnn.so.8: > cannot open shared object file: No such file > or directory; LD_LIBRARY_PATH: > /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > For some reason it's looking for libcudnn.so.8 > but the cryolo package should have installed > libcudnn.so.7.1.2 for you. Can you check that > a) you do have libcudnn8 in cryolo-1.7.6 > environment lib folder? I dont know where is > your env is installed. You can activate conda > and "check conda list env" > b) /home/impmc/.local/bin/cryolo_train.py does > not look like a correct path for cryolo env. > The previous command should tell you where it > should be > > In general, my advice would be to not use > eman2 conda for anything except eman. You'd be > better off using a separate miniconda3 > installation. Which conda did you use for > cryolo 1.8? From eman? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > The files that you requested are attached. > Thanks so much again > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 > 6:18:12 PM > *Subject: *Re: [scipion-users] Problems > with CONDA_ACTIVATION_CMD using Cryolo > > Hi, > The config files look ok. Could you attach > run.stderr and run.stdout for the failed > protocol? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > Thank you so much, fixing this space > solved the problem with > cryolo_1.7.6_installing (shame on me > for this). > However, I tried to run the cryolo > training and I obtained the same > previous error: > > eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&& conda > activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g > 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&& conda > activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g > 0 1 -nc 4 -e 10 --fine_tune' returned > non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, > step 3, time 2021-09-30 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = > ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = > http://scipion.i2pc.es/getplugins/ > <http://scipion.i2pc.es/getplugins/> > SCIPION_SOFTWARE = > ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = > sc...@cn... > <mailto:sc...@cn...> > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = > ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = > http://scipion.cnb.csic.es/downloads/scipion > <http://scipion.cnb.csic.es/downloads/scipion> > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > <http://scipion.cnb.csic.es/downloads/scipion/software> > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > <http://scipion.cnb.csic.es/downloads/scipion/data/tests> > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = > %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate > cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda > activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = > %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = > /usr/local/cuda/lib64 > MOTIONCOR2_HOME = > %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 > 5:51:06 PM > *Subject: *Re: [scipion-users] > Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hello Carlos, > > to start, you are missing a space > between eval and the rest in: > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > Thanks for the message. The all > output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python > -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: > https://pypi.org/simple > <https://pypi.org/simple>, > https://pypi.ngc.nvidia.com > <https://pypi.ngc.nvidia.com> > Requirement already satisfied: > scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages > (3.0.7) > Requirement already satisfied: > scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages > (from scipion-em-sphire==3.0.7) > (3.0.13) > Requirement already satisfied: > biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (1.76) > Requirement already satisfied: > tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (2021.4.8) > Requirement already satisfied: > scipion-pyworkflow>=3.0.15 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (3.0.17) > Requirement already satisfied: > numpy in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) > (1.18.4) > Requirement already satisfied: > mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.0.3) > Requirement already satisfied: > configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.0.0) > Requirement already satisfied: > psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.7.0) > Requirement already satisfied: > pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (7.1.2) > Requirement already satisfied: > bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.2.0) > Requirement already satisfied: > requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.25.1) > Requirement already satisfied: > matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.2.2) > Requirement already satisfied: > tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.1.3) > Requirement already satisfied: > cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: > python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 > in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: > kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: > future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six > in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: > certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: > urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: > chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: > idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v > /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir > /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf > void.tgz -C cryolo-1.7.6 > All targets exist. > cd > /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed > /bin/sh: 1: evalexport > CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export > CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: > BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is > python.exe and on Windows > # it is in a different > relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ > -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; > then > \rehash > elif [ -n "${POSH_VERSION:+x}" > ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n > "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from > shell activated with conda <= 4.3 > to a subsequent activation > # after conda updated to > >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" > __conda_exe shell.posix "$@")" || > \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" > __conda_exe shell.posix > reactivate)" || \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is > python.exe and on Windows > # it is in a different > relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && > [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname > "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be > unbound. It must at least be set. > # However, we're not exporting > it, which can cause problems when > starting a second shell > # via a first shell (i.e. > starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', > numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' > not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed') > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, > 2021 5:33:09 PM > *Subject: *Re: [scipion-users] > Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Dear Carlos, > given the fact that the > installation has failed, could you > attach all output after "scipion3 > installp -p > scipion-em-sphire" command? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:03 PM > Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear all, > > I'm facing some problems using > cryolo training at Scipion. > I found the following error: > *Protocol failed: Command ' > source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& > conda activate cryolo-1.7.6 && > cryolo_train.py -c config.json > -w 5 -g 0 -nc 4 -e 10 > --fine_tune' returned non-zero > exit status 127. > * > * > * > I saw some discussion about > that at Scipion lists, but I'm > still little lost in how to > fix it. > In my scipion.conf file, I > inserted > /CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh > /// > or even > CONDA_ACTIVATION_CMD = > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)"// > (I saw these pathways in my > bash.rc) > > Moreover, when I try to > install cryolo using command > line (scipion3 installp -p > scipion-em-sphire), the > following error apears: > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda > create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 > &&touch cryolo_1.7.6_installed')* > > I am not sure if these errors > are related and hinder > performing cryolo in Scipion. > I have conda installed in the > computer and I'm able to use > cryolo 1.8 outside from > Scipion in the same computer > (using /source activate cryolo > /command). > > Anyone know what I'm doing > wrong? Thanks in advance, Carlos. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > Pablo Conesa - *Madrid Scipion > <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sour... 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